Week 5

This page is under construction.

This journal entry is due on Tuesday, October 3, at 12:01 AM PDT.

Objectives

The purpose of this assignment is:

• to deeply explore and perform a critical review of an existing biological database.
• to communicate your findings in an effective oral presentation.
• to gain and perform a self-assessment of your scientific data literacy skills.

Individual Journal Assignment

• Store this journal entry as "username Week 5" (i.e., this is the text to place between the square brackets when you link to this page).
• Link from your user page to this Assignment page.
• Link to your journal entry from your user page.
• Link back from your journal entry to your user page.
• Don't forget to add the "Journal Entry" category to the end of your wiki page.
  • Note: You can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
• For your assignment this week, you will keep an electronic laboratory notebook on your individual wiki page. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.
  • To be clear, on your individual wiki page, you will document your individual process in your electronic lab notebook.
  • From this week onward, please use the individual journal page for your electronic lab notebook instead of a separate notebook page.

Homework Partners

For most weeks in the semester, you will be assigned a "homework partner" from a complementary discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment. Homework partners for this week are:

• Eddie Azinge, Mary Balducci
• Eddie Bachoura, Emma Tyrnauer
• Dina Bashoura, Nicole Kalcic
• Blair Hamilton, Corinne Wong
• Hayden Hinsch, Simon Wroblewski
• Arash Lari, Antonio Porras
• Quinn Lanners, John Lopez
• Zach Van Ysseldyk, Katie Wright

NAR Database Evaluation and Presentation

Each year, the journal Nucleic Acids Research (NAR) devotes the first issue in January to biological databases. The Week 4 Assignment introduced you to four "gold standard" biological databases. In this assignment you will use what you learned to evaluate a different biological database. Collectively, through presentations, you will gain experience with the breadth and depth of biological databases available on the Web:

• Read (if you haven't already done so):
  • Introduction to the 2017 NAR Database Issue: Galperin, M. Y., Fernández-Suárez, X. M., & Rigden, D. J. (2016). The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic acids research, 45(D1), D1-D11. doi:10.1093/nar/gkw1188
  • Slides from DataONE.org
    • DataONE: Why Data Management
    • DataONE: Data Sharing
• Together with your partner, choose your database:
  • Nucleic Acids Research Database Issue Table of Contents 2017
  • Nucleic Acids Research Database Issue Database List
    • Make sure that the database you choose has a corresponding paper in the 2017 issue.
    • You may not choose a database from NCBI, EBI, or the DNA Databank of Japan. You may not choose Ensembl, UniProt, SGD or another major model organism database. The intent for this exercise is to pick something that is not one of the "major" databases.
    • Sign up for your database by editing this page next to you and your partner's names. Dr. Dahlquist must approve all database choices.

PowerPoint Presentation

Each group will prepare and give a 12-15 minute PowerPoint presentation based on their assigned database in class on Thursday, October 8.

• You will need to prepare ~12-15 slides (assume 1 slide per minute of presentation).
  • Please follow the Presentation Guidelines for how to format your slides.
  • You may give a live demo of the database if you wish, but practice carefully so that you can do the presentation in 15 minutes.
    • Alternately, you may choose to show screen shots instead of the live demo.
• You need to present the information you gathered about your database that you listed in your review above, but organized as a presentation.
• Your presentation (both the slides and the oral presentation) will be evaluated by the instructors using the guidelines shown here in the four areas:
  • Content and message
  • Organization
  • Visuals/slides
  • Speaking style/delivery
• Your PowerPoint slides must be uploaded and shared with the instructors via Please submit your review via LionShare by midnight Thursday (Wednesday night/Thursday morning).
  • You can update your slides before your presentation, but we will be grading the ones you upload by the deadline.
• Finally, your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
  1. What is the speakers’ take-home message? (One short sentence)
  2. What is the best point about the presentation’s organization? What needs improvement? Give one specific example for each.
  3. What is the best point about the presentation’s visuals (slides)? What needs improvement? Give one specific example for each.
  4. What is the best point about the presentation’s delivery (speaking style)? What needs improvement? Give one specific example for each for each presenter.

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 5 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first 👏🏼)
• Link to your journal entry from your user page.
• Link back from the journal entry to your user page.
  • NOTE: You can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
• Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
• Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).